Worst year in review

December 31, 2016December 31, 2016 / zcofran / Leave a comment

As we’re wrapping up what may be the worst year in recent global memory, especially geopolitically, let’s take a moment to review some more positive things that came up at Lawnchair in 2016.

Headed home

Alternate subtitle: Go West
This was a quiet year on the blog, with only 18 posts compared with the roughly thirty per year in 2014-2015. The major reason for the silence was that I moved from Kazakhstan back to the US to join the Anthropology Department at Vassar College in New York. With all the movement there was less time to blog. Much of the second half of 2016 was spent setting up the Biological Anthropology Lab at Vassar, which will focus on “virtual” anthropology, including 3D surface scanning…

Cast of early Homo cranium KNM-ER 1470 and 3D surface scan made in the lab using an Artec Spider.

… and 3D printing.

A gibbon endocast, created from a CT scan using Avizo software and printed on a Zortrax M200.

This first semester stateside I reworked my ‘Intro to Bio Anthro’ and ‘Race’ courses, which I think went pretty well being presented to an American audience for the first time. The latter class examines human biological variation, situating empirical observations in modern and historical social contexts. This is an especially important class today as 2016 saw a rise in nationalist and racist movements across the globe. Just yesterday Sarah Zhang published an essay in The Atlantic titled, “Will the Alt-right peddle a new kind of racist genetics?” It’s a great read, and I’m pleased to say that in the Race class this semester, we addressed all of the various social and scientific issues that came up in that piece. Admittedly though, I’m dismayed that this scary question has to be raised at this point in time, but it’s important for scholars to address and publicize given our society’s tragically short and selective memory.

So the first semester went well, and next semester I’ll be teaching a seminar focused on Homo naledi and a mid-level course on the prehistory of Central Asia. The Homo naledi class will be lots of fun, as we’ll used 3D printouts of H. naledi and other hominin species to address questions in human evolution. The Central Asia class will be good prep for when I return to Kazakhstan next summer to continue the hunt for human fossils in the country.

Osteology is still everywhere

A recurring segment over the years has been “Osteology Everywhere,” in which I recount how something I’ve seen out and about reminds me of a certain bone or fossil. Five of the blog 18 posts this year were OAs, and four of these were fossiliferous: I saw …

Anatomy terminology hidden in 3D block letters,

Hominin canines in Kazakhstani baursaki cakes,

The Ardipithecus ramidus ilium in Almaty,

A Homo naledi juvenile femur head in nutmeg,

And a Homo erectus cranium on a Bangkok sidewalk. As I’m teaching a fossil-focused seminar next semester, OA will probably become increasingly about fossils, and I’ll probably get my students involved in the fun as well.

New discoveries and enduring questions

The most-read post on the blog this year was about the recovery of the oldest human Nuclear DNA, from the 450,000 year old Sima de los Huesos fossils. My 2013 prediction that nuclear DNA would conflict with mtDNA by showing these hominins to be closer to Neandertals than Denisovans was shown to be correct.

These results are significant in part because they demonstrate one way that new insights can be gained from fossils that have been known for years. But more intriguingly, the ability of researchers to extract DNA from exceedingly old fossils suggests that this is only the tip of the iceberg.

The other major discoveries I covered this year were the capuchin monkeys who made stone tools and the possibility that living humans and extinct Neandertals share a common pattern of brain development.

An unrelated image from 2016 that makes me laugh.

The comparison between monkey-made and anthropogenic stone tools drives home the now dated fact that humans aren’t the only rock-modifiers. But the significance for the evolution of human tool use is less clear cut – what are the parallels (if any) in the motivation and modification of rocks between hominins and capuchins, who haven’t shared a common ancestor for tens of millions of years? I’m sure we’ll hear more on that in the coming years.

In the case of whether Neandertal brain development is like that of humans, I pointed out that new study’s results differ from previous research probably because of differences samples and methods. The only way to reconcile this issue is for the two teams of researchers, one based in Zurich and the other in Leipzig, to come together or for a third party to try their hand at the analysis. Maybe we’ll see this in 2017, maybe not.

There were other cool things in 2016 that I just didn’t get around to writing about, such as the publication of new Laetoli footprints with accompanying free 3D scans, new papers on Homo naledi that are in press in the Journal of Human Evolution, and new analysis of old Lucy (Australopithecus afarensis) fossils suggesting that she spent a lifetime climbing trees but may have sucked at it. But here’s hoping that 2017 tops 2016, on the blog, in the fossil record, and basically on Earth in general.

Osteology Everywhere: Skull in the Stone #FossilFriday edition

December 23, 2016December 23, 2016 / zcofran / 2 Comments

It’s that time of year again.

233313fc41ee3a63_tumblr_mgdqksndiz1ro7sbfo1_400-xxxlarge

It’s the end of the year and I’ve got Homo erectus on the brain somethin fierce. Our precedent-erect first popped up in Africa around 1.9 million years ago, quickly spread throughout much of the Old World, and persisted until perhaps as late as ~ 100,000 years ago in Java, Indonesia. This was a very successful species by all accounts, and as a result of its great range and duration, you can imagine it was also pretty variable.

Hominin brain sizes. Boxes and whiskers represent sample tendencies and points are individual specimens. 1 = Australopithecus, 2 = Early Homo (cf. habilis & rudolfensis), 3 = Dmanisi H. erectus, 4 = Early African H. erectus, 5 = Early Indonesian H. erectus, 6 = Chinese H. erectus, 7 = Later Indonesian H. erectus, 8 = modern humans.

Despite this great variation, H. erectus skulls generally share a common visage: long and low cranial vault, low forehead, protruding brow ridges, fun tuberosities and tori in the back. You’d recognize them anywhere. Including the sidewalk!

Homo erectus in front of Ploenchit Tower, Bangkok (lateral view, front is to the right).

The relief in this sidewalk slat superficially looks like a trace fossil of partial H. erectus cranium, the face either missing (from the lower right) or taphonomically displaced toward the left side of the tile (see here for actual H. erectus trace fossils). This looks really similar to H. erectus from Indonesia, not surprising given its discovery in Thailand. Why, it could have come straight out of Figure 6 from a 2006 paper by Yousuke Kaifu and colleagues:

Left lateral views of Javanese H. erectus crania, modestly modified from Kaifu et al. (2006: Fig. 6). Front is to the left this time.

Using my insane photo editing skills, I’ve inserted the Ploenchit Tower trace fossil (reversed) within the horde of heads presented by Kaifu et al., above. Like many of the real fossils, the Ploenchit specimen is missing the face (due to taphonomy), the supraorbital torus or brow ridge juts out from a low-rising forehead, and the occipital bone also projects out about from the otherwise rounded contour of the cranium. Note that there is a good deal of variation in each of these features among the real fossils.

What a happy holiday accident to find a Homo erectus cranium on the street!

seinfeld-its-a-festivus-miracle

Reference
Kaifu Y, Aziz F, Indriati E, Jacob T, Kurniawan I, & Baba H (2008). Cranial morphology of Javanese Homo erectus: new evidence for continuous evolution, specialization, and terminal extinction. Journal of human evolution, 55 (4), 551-80 PMID: 18635247

Osteology Everywhere: Skeletal Spice

November 27, 2016November 27, 2016 / zcofran / 1 Comment

The American winter holiday season is steeped in special spices, such as nutmeg, cloves, cinnamon, and whatever the hell pumpkin spice is. I guess as part of the never-ending War on Christmas, each year this sensory and commercial immersion begins earlier and earlier. Since these have become old news, I’d pretty much forgotten about the seasonal spicecapade until just the other day. In prep for minor holiday gluttony, I was grinding fresh nutmeg when I made a startling discovery. Nutmeg is not just the fragrant fruit of the Myristica fragrans tree. No, there’s something far more sinister in this holiday staple.

Merely nutmeg?

The ground section looks superficially like an unfused epiphyseal surface, whereas the rounded outer surface is more spherical. It turns out, in the most nefarious of all holiday conspiracies since the War on Christmas, nutmeg halves are nothing more than unfused femur heads! Compare with the epiphyseal surface of this Homo naledi femur head:

Nutmeg (left) and H. naledi specimen UW 101-1098 (right).

This immature H. naledi specimen was recently published (Marchi et al., in press), and the associated 3D surface scan has been available for free download on Morphosource.org for a while now. It fits onto a proximal femur fragment, UW 101-1000, also free to download from Morphosource.

Modified Fig. 11 from Marchi et al. It’s weird that only H. naledi bones were found in the Dinaledi chamber, but even weirder is the underreported presence of nutmeg.

Like most bones in the skeleton, the femur is comprised of many separate pieces that appear and fuse together at different, fairly predictable ages. The shaft of the femur appears and turns to bone before birth, and the femur head, which forms the ball in the hip joint, usually appears within the first year of life and fuses to the femur neck in adolescence (Scheuer and Black, 2000). So we know this H. naledi individual was somewhere between 1–15ish years by human standards, probably in the latter half of this large range.

So there you have it. Osteology is everywhere – the holidays are practically a pit of bones if you keep your eyes open.

REFERENCES

Marchi D, Walker CS, Wei P, Holliday TW, Churchill SE, Berger LR, & DeSilva JM (2016). The thigh and leg of Homo naledi. Journal of Human Evolution PMID: 27855981.

Scheuer L and Black S. 2000. Developmental Juvenile Osteology. New York: Elsevier Academic Press.

What do capuchin stone tools tell us about human evolution?

October 20, 2016October 20, 2016 / zcofran / 1 Comment

A month ago at ESHE and now online in Nature, Proffitt and colleagues describe stone-on-stone smashing behavior among wild bearded capuchin monkeys (Sapajus libidinosus). The online paper includes a great video documenting the action; here’s a screenshot:

Holding the rock with both hands just above head-level, the monkey prepares to crush its enemies. Which in this case are another rock stuck in a pile of more rocks.

In the fairly rare cases where non-human primates use stones, it’s for smashing nuts or something. But when these capuchins see a stone they don’t just see a smasher, they see a world of possibilities* – why use a rock to break a rock, when you could use it to break a heart? So this group of capuchins is unique in part because they’ve been documented to use stones for many purposes.

Now why on earth a monkey would use one rock to break another rock is anyone’s guess. In human evolution, the purpose was to break off small, sharp flakes that could be used to butcher animals or work plants. Proffitt et al. did observe small flakes being removed when capuchins pounded rocks, but the monkeys showed little interest in this debitage, other than using it to continue smashing stuff. More curiously, the monkeys frequently lick the rock after hammering at it:

Mmm, rocks.

Proffitt et al. venture that maybe these monkeys are doing this to ingest lichens or trace elements like silicon. This hypothesis merits further investigation, but what’s clear is that these monkeys’ lithics differ from the hominin archaeological record wherein the express purpose of breaking rocks is to make flakes.

What’s striking to me (pun intended) is the relative size of the rocks. These monkeys that weigh only 2-3 kg are lifting and smashing stones that weigh about half a kilogram on average. Because these stones are fairly large given the monkeys’ body size, they have to be lifted with two hands and brought down on a surface, a “passive hammer” technique. The earliest-known tools made by hominins, from the 3.3 million year old Lomekwi site in Kenya, are also pretty big. Weighing 3 kg on average but topping at 15 kg, these earliest tools would have required the same knapping technique as is used by these little monkeys (Harmand et al., 2015).

Left: Cover of Nature vol. 521 (7552). Right: Bearded capuchin letting a pebble know who’s boss (link).

Why the big stuff at first? Did the earliest hominin tool-makers lack the dexterity to make tools from the smaller rocks comprising the later Oldowan industry? These creative capuchins could lead to predictions about the hand/arm skeleton of the Lomekwian tool-makers (testable, of course, only with fortuitous fossil discoveries). Capuchins are noted for their manual dexterity (Truppa et al., 2016) and have a similar thumb-index finger ratio to humans and early hominins (Feix et al. 2015), although they differ from humans in the insertion of the opponens muscle and resultant mobility of the thumb (Aversi-Ferreira et al., 2014). Maybe these tech-smart monkeys can tell us more about the earliest human tool-makers’ bodies than their brains.

References

Aversi-Ferreira RA, Souto Maior R, Aziz A, Ziermann JM, Nishijo H, Tomaz C, Tavares MC, & Aversi-Ferreira TA (2014). Anatomical analysis of thumb opponency movement in the capuchin monkey (Sapajus sp). PloS one, 9 (2) PMID: 24498307

Feix T, Kivell TL, Pouydebat E, & Dollar AM (2015). Estimating thumb-index finger precision grip and manipulation potential in extant and fossil primates. Journal of the Royal Society, Interface, 12 (106) PMID: 25878134

Harmand S, Lewis JE, Feibel CS, Lepre CJ, Prat S, Lenoble A, Boës X, Quinn RL, Brenet M, Arroyo A, Taylor N, Clément S, Daver G, Brugal JP, Leakey L, Mortlock RA, Wright JD, Lokorodi S, Kirwa C, Kent DV, & Roche H (2015). 3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya. Nature, 521 (7552), 310-5 PMID: 25993961

Proffitt, T., Luncz, L., Falótico, T., Ottoni, E., de la Torre, I., & Haslam, M. (2016). Wild monkeys flake stone tools Nature DOI: 10.1038/nature20112

Truppa V, Spinozzi G, Laganà T, Piano Mortari E, & Sabbatini G (2016). Versatile grasping ability in power-grip actions by tufted capuchin monkeys (Sapajus spp.). American Journal of Physical Anthropology, 159 (1), 63-72 PMID: 26301957

*well, at least four uses given by Proffitt et al.: mating display, aggression, food-crushing, and digging.

A change of scenery

October 17, 2016October 17, 2016 / zcofran / 1 Comment

It’s been quiet here as I’ve been moving the Lawnchair all over the place since the summer and haven’t had time to write. Bittersweetly no longer in Kazakhstan, I’ve just joined the Anthropology Department at Vassar College in New York. Here’s a quick, summery summary of one of the last things I did as an immigrant in Central Asia.

Site search: No end in sight

The yellow pin marks the location of our survey. This is very close to the Polygon, a nuclear test site used during Soviet times.

In early June some colleagues and I ventured to East Kazakhstan in search of caves that earlier humans might have called home. Our initial plan was to visit the Altai Mountains, but permits fell through at the last minute. Fortunately, Bronze Age archaeologists from Eurasian National University and University of Semipalatinsk told us of some caves near where they were working in the Shyngystau region, and let us set up camp with them.

Lightning strikes behind the karstic, cave-pocked uplift by our campsite.

Abutting Bronze Age burial mounds and just a small hike to a large recent cemetery, the campsite was flanked by thousands of years of burial practices. Would the nearby caves push this boundary into the Stone Age?

Looking south from the previously pictured caves. Trees mark the course of a braided stream, and in the distance you can barely make out the mausoleum-filled cemetery. Camp is just off-camera to the right.

We found and explored a number of shallow caves in the area, but unfortunately none of these were productive Paleolithic sites. This rocky uplift (below), for instance, was adjacent to a meandering stream that probably gets pretty deep during flood season. The water had carved out one small cave (bottom right), and there was a larger, south-facing cave just above ground level.

The larger cave funneled into an enticingly narrow crawlspace. On the principle of “if you don’t look, you’ll never know,” and inspired by the geological situation of Homo naledi, we figured it was worth at least looking.

Into the crevasse.

WRONG! It ended when I was only a little over a body length in. But again, if you don’t look, you’ll never know. What you will come to know, however, is how many and what size of spiders are in cave; the result is always upsetting.

Spiders 2.JPG

While the trip didn’t go exactly as planned, it was still highly informative to see more of the geology of East Kazakhstan. Fortunately, we have received funding from the Growth Development and Research Institute of Nazarbayev University, to begin survey of the Bukhtarma River Valley as we’d initially intended. Hopefully next summer we’ll see more caves, exciting finds, and fewer spiders.

Dietary divergence of robust australopithecines

July 28, 2016July 29, 2016 / zcofran / Leave a comment

I’m writing a review of the “robust” australopithecines, and I’m reminded of how drastically our understanding of these hominins has changed in just the past decade. Functional interpretations of the skull initially led to the common wisdom that these animals ate lots of hard foods, and had the jaws and teeth to cash the checks written by their diets.

Comparison of a “gracile” (left) and “robust” (right) Australopithecus face, from Robinson (1954).

While anatomy provides evidence of what an animal could have been eating, there is more direct evidence of what animals actually did eat. Microscopic wear on teeth reflects what kinds of things made their way into an animal’s mouth, presumably as food, and so provide a rough idea of what kinds of foods an animal ate in the days before it died. Microwear studies of A. robustus from South Africa had confirmed previous wisdom: larger pits and more wear complexity in A. robustus than in the earlier, “gracile” A. africanus suggested more hard objects in the robust diet (e.g., Scott et al., 2005). A big shock came a mere 8 years ago with microwear data for the East African “hyper robust” A. boisei: molars had many parallel scratches and practically no pitting, suggesting of a highly vegetative diet (Ungar et al. 2008).

Microwear in A. boisei (blue) and A. robustus (red). Although they overlap mostly for anisotropy (y-axis), they are completely distinct for complexity (x-axis). Data from Grine et al. (2012) and skull diagrams from Kimbel et al. (2004).

Stable carbon isotope analysis, which assesses what kinds of plant-stuffs were prominent in the diet when skeletal tissues (e.g. teeth) formed, further showed that the two classically “robust” hominins (and the older, less known A. aethiopicus) ate different foods. Whereas A. robustus had the carbon isotope signature of an ecological generalist, A. boisei had values very similar to gelada monkeys who eat a ton of grass/sedge. GRASS!

Stable carbon isotope data for robust australopithecines. Data from Cerling et al. (2013) and skull diagrams from Kimbel et al. (2004). Note again the complete distinction between A. robustus (red) and A. boisei (blue).

While microwear and isotopes don’t tell us exactly what extinct animals ate, they nevertheless are much more precise than functional anatomy and help narrow down what these animals ate and how they used their environments. This highlights the importance of using multiple lines of evidence (anatomical, microscopic, chemical) to understand life and ecology of our ancient relatives.

REFERENCES

Cerling TE, Manthi FK, Mbua EN, Leakey LN, Leakey MG, Leakey RE, Brown FH, Grine FE, Hart JA, Kaleme P, Roche H, Uno KT, & Wood BA (2013). Stable isotope-based diet reconstructions of Turkana Basin hominins. Proceedings of the National Academy of Sciences, 110 (26), 10501-6 PMID: 23733966

Grine FE, Sponheimer M, Ungar PS, Lee-Thorp J, & Teaford MF (2012). Dental microwear and stable isotopes inform the paleoecology of extinct hominins. American Journal of Physical Anthropology, 148 (2), 285-317 PMID: 22610903

Kimbel WH, Rak Y, & Johanson DC (2004). The Skull of Australopithecus afarensis. Oxford University Press.

Robinson, J. (1954). Prehominid Dentition and Hominid Evolution Evolution, 8 (4) DOI: 10.2307/2405779

Ungar PS, Grine FE, & Teaford MF (2008). Dental microwear and diet of the Plio-Pleistocene hominin Paranthropus boisei. PloS One, 3 (4) PMID: 18446200

Did Neandertal brains grow like humans’ or not?

July 26, 2016July 26, 2016 / zcofran / 1 Comment

According to Marcia Ponce de Leon and colleagues, “Brain development is similar in Neandertals and modern humans.” They reached this conclusion after comparing how the shape of the brain case changes across the growth period of humans and Neandertals. This finding differs from earlier studies of Neandertal brain shape growth (Gunz et al. 2010, 2012).

Although Neandertals had similar adult brain sizes as humans do today, the brains are nevertheless slightly different in shape:

Endocranial surfaces of a human (left, blue) and Neandertal (right, red), from Gunz et al. (2012). These surfaces reflect the size and shape of the brain, blood vessels, cerebrospinal fluid, and meninges.

Gunz et al. (2010, 2012) previously showed that endocranial development in humans, but not in Neandertals or chimpanzees, has a “globularization phase” shortly after birth: the endocranial surface becomes overall rounder, largely as a result of the expansion of the cerebellum:

Endocranial (e.g., brain) shape change in humans (blue), Neandertals (red) and chimpanzees (green), Fig. 7 from Gunz et al. (2012). Age groups are indicated by numbers. The human “globularization phase” is represented by the great difference in the y-axis values of groups 1-2 (infants). The Neandertals match the chimpanzee pattern of shape change; Neandertal neonates (LeM2 and M) do not plot as predicted by a human pattern of growth.

Ponce de Leon and colleagues now challenge this result with their own similar analysis, suggesting similar patterns of shape change with Neandertals experiencing this globularization phase as well (note that endocranial shapes are always different, nevertheless):

Endocranial shape change in humans (green) and Neandertals (red), from Ponce de Leon et al. (2016). Note that the human polygons and letters represent age groups, whereas the Neandertal polygons and labels are reconstructions of individual specimens.

The biggest reason for the difference between studies is in the fossil sample. Ponce de Leon et al. have a larger fossil sample, with more non-adults including Dederiyeh 1-2, young infants in the age group where human brains become more globular.

Comparison of fossil samples between the two studies.

But I don’t think this alone accounts for the different findings of the two studies. Overall shape development is depicted in PC 1: in general, older individuals have higher PC1 scores. The globularization detected by Gunz et al. (2010; 2012) is manifest in PC2; the youngest groups overlap entirely on PC1. The biggest difference I see between these studies is where Mezmaiskaya, a neonate, falls on PC2. In the top plot (Gunz et al., 2012), both Mezmaiskaya and the Le Moustier 2 newborn have similar PC2 values as older Neandertals. In the bottom plot (Ponce de Leon et al., 2012), the Mezmaiskaya neonate has lower PC2 scores than the other Neandertals. Note also the great variability in Mezmaiskaya reconstructions of Ponce de Leon et al. compared with Gunz et al.; some of the reconstructions have high PC2 values which would greatly diminish the similarity between samples. It’s also a bit odd that Engis and Roc de Marsal appear “younger” (i.e., lower PC1 score) than the Dederiyeh infants that are actually a little bit older.

Ponce de Leon et al. acknowledge the probable influence of fossil reconstruction methods, and consider other reasons for their novel findings, in the supplementary material. Nevertheless, a great follow-up to this, to settle the issue of Neandertal brain development once and for all, would be for these two research teams to join forces, combining their samples and comparing their reconstructions.

REFERENCES

Gunz P, Neubauer S, Maureille B, & Hublin JJ (2010). Brain development after birth differs between Neanderthals and modern humans. Current Biology : 20 (21) PMID: 21056830

Gunz P, Neubauer S, Golovanova L, Doronichev V, Maureille B, & Hublin JJ (2012). A uniquely modern human pattern of endocranial development. Insights from a new cranial reconstruction of the Neandertal newborn from Mezmaiskaya. Journal of Human Evolution, 62 (2), 300-13 PMID: 22221766

Ponce de León, M., Bienvenu, T., Akazawa, T., & Zollikofer, C. (2016). Brain development is similar in Neanderthals and modern humans Current Biology, 26 (14) DOI: 10.1016/j.cub.2016.06.022

The strange days of yore

June 23, 2016June 23, 2016 / zcofran / Leave a comment

Today is not like the good ol’ days. In many ways things have changed for the better. For instance, in the good ol’ days, many paleontologists would find fossils but let nary a soul examine them; today, you can download high quality 3D models of many important fossils from both East and South Africa, completely for free!

Robert Broom’s (1938) account of the discovery of the first Paranthropus (or Australopithecus) robustus is also a reminder of the strangeness of the bygone days of yore:

Wait for it …

In June of this year a most important discovery was made. A schoolboy, Gert Terblanche, found in an outcrop of bone breccia near the top of a hill, a couple of miles from the Sterkfontein caves, much of the skull and lower jaw of a new type of anthropoid. Not realizing the value of the find, he damaged the specimen considerably in hammering it out of the rock. The palate with one molar tooth he gave to Mr. Barlow at Sterkfontein, from whom I obtained it. Recognizing that some of the teeth had recently been broken off, and that there must be other parts of the skull where the palate was found, I had to hunt up the schoolboy. I went to his home two miles off and found that he was at the school another two miles away, and his mother told me that he had four beautiful teeth with him. I naturally went to the school, and found the boy with four of what are perhaps the most valuable teeth in the world in his trouser pocket. He told me that there were more bits of the skull on the hillside. After school he took me to the place and I gathered every scrap I could find; and when these were later examined and cleaned and joined up, I found I had not only the nearly perfect palate with most of the teeth, but also practically the whole of the left side of the lower half of the skull and the nearly complete right lower jaw.

What a wild time – Broom hunts down poor Gert, barges into the school, then makes the kid show him where he hacked the skull out of the rock. Poor, poor Gertie.

Maybe it was a different Gertie, but surely the reaction was the same.

Of course, there was a lot at stake. I mean, brazen Gert harbored not just “beautiful teeth,” but “the most valuable teeth in the world.” IN HIS TROUSERS! And of course Gert was also the soul possessor of priceless intel – the source of the fossils. So maybe Broom was justified in this zealous abduction. And O! such prose in a Nature paper! WAS IT WORTH IT, DR. BROOM?

At Sterkfontein, a bronzed Broom considers the weight of his actions.

Of course, Gert wasn’t the last kid to discover an important human fossil. The game-changing Australopithecus sediba was discovered when Matthew Berger, son of famed Lee Berger and only 9 years old at the time, saw a piece of a clavicle sticking out of a block of breccia. Both Gert and Matthew show that you don’t have to be a doctor to make amazing discoveries. What future fossil discoveries will be made by kids, and making my adult accomplishments pale in comparison?!

Osteology Everywhere: Ardipithecus in Almaty?

June 2, 2016June 2, 2016 / zcofran / 1 Comment

A few weeks ago I was traipsing across Almaty, Kazakhstan’s former capital, when a stain in the road caught my eye:

Roadside osteology. The intersection of the trunk and legs at the intersection of Abay & Seifullin?

It’s obviously iliac but it’s not just any old ilium. I think I discovered the underreported antimere of the Ardipithecus ramidus pelvis (ARA-VP 6/500; Lovejoy et al., 2009). What it’s doing in Almaty, and in the middle of a busy street, I have no idea. I’ve long thought the absence of hominin fossils in Kazakhstan was suspicious. But not this suspicious.

Roadside paleontology. The Almaty Ardi innominate (left), compared with the actual ARA-VP-1/500 innominate (center) and its reconstruction (right). Adapted from Lovejoy et al. 2009.

Roadside paleontology. The Almaty intersection innominate (left), compared with the actual ARA-VP-1/500 innominate (center) and its reconstruction (right). Adapted from Lovejoy et al. 2009.

The Ardi innominate pictured (center, above) is from the left side, and the Almaty intersection innominate is a perfect counterpart from the right. Yes, I know they found a right ilium at Aramis to go with the better preserved left half. But to that I reply:

Let’s compare the “true” right ilium from Aramis (left, below) with my more likely antimere (right). Look how perfectly the Almaty Ardi fits the reconstruction:

Aramis innominate fossils (left) compared with the Almaty Ardi roadside fragment overlain on the reconstructed pelvis (right).

The lower portion of the ilium is a bit taller than in later hominins, what’s preserved of the acetabulum is a bit small, and there’s a beautiful portion of the auricular surface for articulation with the (never recovered) sacrum. I rest my case.

Despite their strange shapes, pelvic parts seem to be the epitome of “osteology everywhere.”

Reference
Lovejoy CO, Suwa G, Spurlock L, Asfaw B, & White TD (2009). The pelvis and femur of Ardipithecus ramidus: the emergence of upright walking. Science (New York, N.Y.), 326 (5949), 710-6 PMID: 19810197

You can read the media summaries (not actual articles) of the Ardipithecus ramidus reports here.

Materials from the R workshop at #AAPA2016

April 18, 2016April 18, 2016 / zcofran / 1 Comment

For last week’s AAPA conference, my friend and colleague David Pappano organized a workshop teaching about the many uses of the R programming language for biological anthropology (I’m listed as co-organizer, but really David did everything). After introducing the basics, we broke into small groups focusing on specific aspects of using R. I devised some lessons for basic statistics, writing functions, and resampling. Since each of the lessons could have easily taken up an hour and most people didn’t get to go through the activities fully, I’m posting up the R codes here for people to mess around with.

The basic stats lesson utilized Francis Galton’s height data for hundreds of families, courtesy of Dr. Ryan Raaum. To load in these data you just need to type into R: galton = read.csv(url(“http://bit.ly/galtondata“)). The code simply shows how to do basic statistics that are built into R, such as t-test and linear regression.

Example of some summary stats for the Galton height data.

Some summary stats for the Galton data. The code is in blue and the output in black.

Here is the Basic Stats code, download and paste it into an R file, then buckle up!

The lesson on functions and resampling was based on limb length data for apes, fossil hominins and modern humans (from Dr. Herman Pontzer). The csv file with the data can be downloaded from David’s website. R has lots of great built-in functions (see basic stats, above), and even if you’re looking to do something more than the basics, chances are you can find what you’re looking for in one of the myriad packages that researchers have developed and published over the years. But sometimes it’s necessary to write a function on your own, and with fossil samples you may find yourself needing to do resampling with a specific function or test statistic.

For example, you can ask whether a small sample of “anatomically modern” fossil humans (n=12) truly differs in femur length from a small sample of Neandertals (n=9). Traditional statistics require certain assumptions about the size and distribution of the data, which fossils fail to meet. Another way to ask the question is, “If the two groups come from the same distribution (e.g. population), would random samples of sizes n=12 and n=9 have so great an average difference as we see between the fossil samples?” A permutation test, shuffling the group membership of the fossils and then calculating the difference between the new “group” means, allows you to quickly and easily ask this question:

R code for a simple permutation test. The built-in function “sample()” is your best friend.

Although simply viewing the data suggests the two groups are different (boxplot on the left, below), the permutation test confirms that there is a very low probability of sampling so great a difference as is seen between the two fossil samples.

Left: Femur lengths of anatomically modern humans (AMH) and Neandertals. Right: distribution of resampled group differences. Dashed lines bracket 95% of the resampled distribution, and the red line is the observed difference between AMH and Neandertal femur lengths. Only about 1% of the resampled differences are as great as the observed fossil difference.

Here’s the code for the functions & resampling lesson. There are a bunch of examples of different resampling tests, way more than we possibly could’ve done in the brief time for the workshop. It’s posted here so you can wade through it yourself, it should keep you busy for a while if you’re new to R. Good luck!

Lawn Chair Anthropology

Biological anthropology, paleontology, evolution, and development, by Dr. Zachary Cofran

Author: zcofran